Jellyfish does multiple sequence alignment. When I wrote the MSA code
(actually, I ported the relevant parts of Clustal W to Java),
Jellyfish was free to use.
"Gordon D. Pusch" wrote:
>> Are there any good multiple alignment tools that are public domain or GPL ???
> CLUSTALW is excellent, but it appears to require a licensing agreement for
> non-academic users...
>> -- Gordon D. Pusch
>> perl -e '$_ = "gdpusch\@NO.xnet.SPAM.com\n"; s/NO\.//; s/SPAM\.//; print;'
"It takes a particularly rarified variety of idiot to look at a
Jew-hating fascist with a small mustache - and decide that his
opponent is the Nazi."